Seagrass ecosystem is one of the ecosystems that has high primary productivity, supported by the presence of periphyton which attached to the seagrass leaf surface. The influence can less result of fishing activity or anthropogenic activities can also cause contamination of heavy metals like a Pb and Cd. The purpose of this research were to determine the type of seagrass, the abundance of perifiton and heavy metal content in the seagrass leaves and relationship periphyton abundance to the heavy metal content in the Gulf of Jepara. This research uses descriptive method. Research activities carried out arround March-April 2016 in the Gulf of Jepara in dense seagrass environment (368 ind/m2), moderate (240 ind/m2), dan rare (178 ind/m2). Determining location of sampling using purposive random sampling method to determine the object sampled by different densities of the seagrass. Seagrass species found in the Gulf of Jepara is Thalassia sp. The average abundance of periphyton in dense, medium and rare seagrass density are 1742 ind/cm2, 1481 ind/cm2, and 1249 ind/cm2. Periphyton types were found came from class of Bacillariophyceae, Cyanophyceae, Euglenophyceae, Rodhophyceae, Dinophyceae and Chlorophyceae. The result of heavy metals Pb and Cd for three times of the sampling obtained similar content of heavy metals which are Pb <100 mg/gr and Cd <10 mg/gr. Based on the research results concluded that content of Pb and Cd heavy metals is not affect the existence periphyton on leaves of seagrass in the Gulf waters Jepara